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Structure of PDB 5nk9 Chain A Binding Site BS01

Receptor Information
>5nk9 Chain A (length=285) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTEIHPSCVTRQKVIGAGEFGEVYKGMLKKEVPVAIKTLKAGYTEKQRVD
FLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDG
EFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFG
LSRVLEDDPEATYTTGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVM
TYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARR
PKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLP
Ligand information
Ligand ID912
InChIInChI=1S/C25H29ClN4O3S/c1-15-5-3-8-19(26)21(15)30-23(32)20-14-27-24(34-20)29-18-7-4-6-16(13-18)22(31)28-17-9-11-25(2,33)12-10-17/h3-8,13,17,20,33H,9-12,14H2,1-2H3,(H,27,29)(H,28,31)(H,30,32)/t17-,20-,25-/m1/s1
InChIKeyNVYXPDJGZNQIHE-FLPMJASOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cccc(Cl)c1NC(=O)[CH]2CNC(S2)=Nc3cccc(c3)C(=O)N[CH]4CC[C](C)(O)CC4
CACTVS 3.385Cc1cccc(Cl)c1NC(=O)[C@H]2CNC(S2)=Nc3cccc(c3)C(=O)N[C@H]4CC[C@](C)(O)CC4
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)C2CN/C(=N/c3cccc(c3)C(=O)NC4CCC(CC4)(C)O)/S2)Cl
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)C2CNC(=Nc3cccc(c3)C(=O)NC4CCC(CC4)(C)O)S2)Cl
FormulaC25 H29 Cl N4 O3 S
Name(2~{Z})-~{N}-(2-chloranyl-6-methyl-phenyl)-2-[3-[(4-methyl-4-oxidanyl-cyclohexyl)carbamoyl]phenyl]imino-1,3-thiazolidine-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain5nk9 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nk9 Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors.
Resolution1.588 Å
Binding residue
(original residue number in PDB)		I619 A644 K646 E663 I690 T692 Y694 M695 G698 K702 L746
Binding residue
(residue number reindexed from 1)		I15 A35 K37 E54 I81 T83 Y85 M86 G89 K93 L137
Annotation score1
Binding affinityMOAD: Kd=0.724uM
PDBbind-CN: -logKd/Ki=6.14,Kd=724nM
Enzymatic activity
Catalytic site (original residue number in PDB) D739 A741 R743 N744 D757 D766 P780
Catalytic site (residue number reindexed from 1) D130 A132 R134 N135 D148 D157 P169
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5nk9, PDBe:5nk9, PDBj:5nk9
PDBsum5nk9
PubMed28544567
UniProtP29317|EPHA2_HUMAN Ephrin type-A receptor 2 (Gene Name=EPHA2)

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